Following the Nightfall Program'sheadquarters being compromised to the government, Castle began investigating Archer's past military experience, as well as his employee Dr. Samantha Cross. Days later, Castle dispatched CIF Team One to the second Cryptid outbreak, intending to locate Cross and kill or capture Archer, now deemed an international terrorist. Under the codename "Godfather", Castle watched his squad's progress, and presumed Cross was among Nightfall's casualties and demanded that Archer was brought out in handcuffs or a bodybag. His claim was quickly proven false when Samantha confirmed she was alive, hiding in the facility's research lab, only to be captured by Archer and taken with him into the Alaskan Frontier. Determined to salvage as much as possible of the mission, Godfather demanded CIF Team One to kill the Breeder. He later extracted his men from the facility's wreckage and began a search for Archer. Following the events of Nightfall, Godfather was relocated to the Exodus Space Station.

Weeks into their search, Godfather was unexpectedly contacted by David Archer himself, intending to form an alliance with his forces against the invading Cryptid threat. Knowing the government would benefit greatly from his knowledge of the creatures, and fearing the President unable to perform the necessary decisions in the war, Castle agreed to extract Archer from his vessel under the condition Cross' severed head was brought with him. After receiving a distress call from Archer's ship, Stormbreaker, now stranded in the Tasman Sea, Castle yet again guided CIF Team One through another Cryptid outbreak, this time intent on killing Cross and saving Archer. After Cross disappeared from the vessel and the Kraken was defeated, Castle immediately evacuated the sinking ship, with Archer being recruited under the name DARPA alongside his soldiers. When Cross' body failed to resurface, he declared her among the deceased, the scene of destruction in the Beacon Chamber attributed to "severe weather". As his men descended on a Cryptid colony beneath Ball's Pyramid, Godfather conversed with an infuriated President, explaining Archer to be a necessary evil in the fight against the alien threat.

A day after the events of Mayday, Godfather oversaw the infiltration of Ball's Pyramid in order to obtain the Cortex biological weapon, having David Archer leading a small team into the depths of the island. However, when Archer and two American soldiers were surrounded, one tried to throw a grenade, but was decapitated by a Gargoyle, thus causing the live grenade to head towards Archer and the other soldier. However, Archer grabbed the soldier and used him to shield the blast The grenade explodes, killing the man and causing Archer's arm to rub against a poisonous Cyptid bush, infecting his arm and causing him to lean on an Obelisk. Suddenly, Samantha Cross appeared and explained to Archer about his wound. Archer then thought that was dreaming, which prompted Cross to then cut off his right arm with her Machete, sparing him and saving him from the infection. Having lost contact with Archer's team, Godfather then sent Rapid Reaction Force - CIF Team 1 again to scan Obelisks, gain access into the Ark, and secure the Cortex. In the epilogue, he and the Rapid Reaction Force fled Ball's Pyramid to the Exodus Launch Site, with Cross in tow.

During Exodus, due to the President being declared K.I.A., he became the man in charge of the fate of the United States as well as the rest of the world. He sent CIF Team 1 in order to power up the generators, which in turn would supply power to the Medusa Device. When the 5th/6th generators were activated, Samantha Cross contacted Godfather, stating that she was going to be boarding the space shuttle. When the CIF Team activated all of the 6 generators, they later met up with Cross at the outpost, where she told them that she'd be boarding the shuttle, and they would not. She then instructed them to defend the Medusa Device while it charged off of the ongoing onslaught of Cryptids and Ancestors and activate it when its fully charged as she prepared to board and launch the space shuttle into space. Realizing that the CIF Team's fate was sealed, he gave out his final instructions to the CIF Team to do as Cross instructed them to do. When the device fully charged, Godfather then shouted out to the CIF Team that they needed to activate the cortex immediately. They did so, and the space shuttle launches, en route to the space station. Godfather is never heard of after the CIF Team activated the device, and sacrificing themselves.

Godfather created the majority of the Intels in Exodus, talking about the Arks, the Ancestors, and the Gargoyles.

"Godfather to CIF Team 1. It's started. Contain the outbreak before it spreads even further. Target the hives first. Deploy the drill and establish a defensive perimeter. If we lose control of the situation, this will end just like Colorado."

— At the start of the game.

"David Archer. He was a top shooter with the SAS until he washed out on a section 8. Now he's the shot caller for the Nightfall outfit. I met Archer during the war. He didn't strike me as the type to crack under pressure. But this tape from his psych evaluation suggests otherwise."

— Castle's thoughts on David Archer in Nightfall intel.

"Samantha Cross. PhD in paleolinguistics. She was a rising star at Harvard before she vanished last year. Cross is some kind of sevant. A natural code breaker. She turned down a seven figure contract with the NSA to dig holes in the jungle. She disappeared a week after this interview aired."

"CIF 1, this is Godfather. We have a category three Cryptid outbreak in progress aboard that ship. Your objective is to rescue a double agent held somewhere inside. Bio-readings suggest we're dealing with new Cryptid lifeforms. You'll know what's waiting for you in there. Keep your head down and your finger on the trigger. Godfather out."

"Godfather to CIF 1. We've been fighting our way up the Cryptid food chain since Colorado, and we've finally made it to the top. You're about to go head to head with the Ancestor race on their home turf. They'll be expecting an attack on the Ark. Let's not disappoint them. Your team has been assigned to a cipher prototype. It's an optical scanner mounted on a modified drill chassis. Use it scan the glyphs on those Obelisks. The cipher uses Cross' translation software to decode the Ancestors' hieroglyphics. Use it to scan the inscriptions on those obelisks."

— At the start of the game.

"Godfather to Strike One, do you copy?"

— In Awakening intel.

"What have you done with Cross?"

— Awakening

"Listen to me Archer. If Cross knows what the Ancestors are planning, she's far more valuable to us alive than dead."

— Awakening

"Negative. You will return Cross to the surface unharmed. That is an or-(static)"

— In Awakening to Archer.

"Copy Archlight. Proceed directly to the Exodus launch site. I'll tell them to save four seats."

— Godfather responding to Archlight.

"I'll be damned."

— After finding out Cross escaped.

"The war is over, sir. We lost. We project eighty percent of the planet's surface will be overrun within two hundred hours."

— To the President in the Awakening cutscene.

"There's only one page left in the playbook - scorched earth."

— To the President.

"The Ancestors survived the last apocalypse in arks hidden under our feet. But we've got an ark of our own... Hanging right over their heads."